The effects of El Nino Modoki events on the tropical tropopause layer (TTL) and on the stratosphere were investigated using European Center for Medium Range Weather Forecasting (ECMWF) reanalysis data, oceanic El Nino indices, and general climate model outputs. El Nino Modoki events tend to depress convective activities in the western and eastern Pacific but enhance convective activities in the central and northern Pacific. Consequently, during El Nino Modoki events, negative water vapor anomalies occur in the western and eastern Pacific upper troposphere, whereas there are positive anomalies in the central and northern Pacific upper troposphere. The spatial patterns of the outgoing longwave radiation (OLR) and upper tropospheric water vapor anomalies exhibit a tripolar form. The empirical orthogonal function (EOF) analysis of the OLR and upper tropospheric water vapor anomalies reveals that canonical El Nino events are associated with the leading mode of the EOF, while El Nino Modoki events correspond to the second mode. The composite analysis based on ERA-interim data indicate that El Nino Modoki events have a reverse effect on middle-high latitudes stratosphere, as compared with the effect of typical El Nino events, i.e., the northern polar vortex is stronger and colder but the southern polar vortex is weaker and warmer during El Nino Modoki events. According to the simulation' results, we found that the reverse effect on the middle-high latitudes stratosphere is resulted from a complicated interaction between quasi-biennial oscillation (QBO) signal of east phase and El Nino Modoki signal. This interaction is not a simply linear overlay of QBO signal and El Nino Modoki signal in the stratosphere, it is El Nino Modoki that leads to different tropospheric zonal wind anomalies with QBO forcing from that caused by typical El Nino, thus, the planetary wave propagation from troposphere to the stratosphere during El Nino Modoki events is different from that during canonical El Nino events. However, when QBO is in its west phase, El Nino Modoki events have the same effect on middle-high latitudes stratosphere as the typical El Nino events. Our simulations also suggest that canonical El Nino and El Nino Modoki activities actually have the same influence on the middle-high latitudes stratosphere when in the absence of QBO forcing.